Plant Molecular Biology and Biotechnology
Engineering Tree Biomass and Plant Oils for Bioenergy
Species Identification Using Molecular Diagnostics
Functional Genomics of Plant-Microbe Interactions
Office: Shelby Center Room 302L
Research in our lab makes use of some of the most advanced modern molecular techniques to address fundamental environmental and social issues. We use a variety of tools and techniques from basic biochemistry and molecular biology to functional genomics, bioinformatics and chemical imaging at the National Synchrotron Light Source to get at the heart of how plants interact with the environment and in turn impact people. Our lab collaborates with a number of other academic and government labs in U.S. and abroad, allowing students and researchers opportunities to visit these other labs and expand and enrich their cultural and research experience. Summaries of our primary projects are as follows:
In recent years, there has been a lot of hype about the need for new sources of fuel. We have all felt the impact of overseas oil issues, hurricanes, oil spills and the subsequent fluctuating prices of petroleum fuels. Our lab is pursuing several projects that focus on the development of better sources of energy. For the last 10 years, our lab has been involved in developing poplar trees for increasing cellulosic biomass for bioenergy. Ongoing projects include the characterization of tree genes that can be used in the development of trees or processes that enhance resistance to pests, oxidative stresses and increase carbon sequestration. Through collaborations with the Department of Energy (DOE), Argonne National Laboratory (ANL) and Brookhaven National Laboratory (BNL) we have performed transcriptomic, proteomic and biochemical studies to elucidate the molecular mechanisms of how different aspen trees have differing abilities to sequester carbon from the atmosphere, especially in response to differing soil microbe communities. To this end, our lab is studying how trees, soil fungi and soil bacteria come together in symbiotic relationships that allow the trees to have access to soil nutrients that would otherwise remained locked in the soil structure. Likewise, our lab has been involved in the first genome-sequencing project of an ectomycorrhizal fungus, Laccaria bicolor, by the Department of Energy Joint Genome Institute. We continue to work in collaboration with ANL to improvement genome annotations through the analysis of symbiotic, plant stress and nutrient related differential gene expression using next generation sequencing. Our aim is to apply such studies towards a Systems Biology level understand of gene function at the organismal level. We often never realize that it is the soil microbe community that often allows each tree to gather nutrients from the environment. Without such beneficial organisms, we would likely have no forests, no wood, no paper, and our environment would suffer greatly.
In addition, our collaborations with Brookhaven National Laboratory and The Energy Resources Institute (TERI) in India aim to use metabolic engineering to generate Jatropha curcas trees with improved or altered oil biosynthetic capacity and tolerance to environmental stresses. Through next generation sequencing and chemical imaging, we have been characterizing the Jatropha biosynthetic pathways as well as regulatory factors involved in cold- and drought-tolerance. We are using such data to target molecular pathways that may be limiting oil biosynthesis or the ability of the trees to grown in certain regions of the world.
Other projects in the lab focus on invasive plant and nematode species and how we can help to prevent their detrimental impact on our environment. With the expanding globalization of trade, the impact of invasive plants continues to increase, costing the U.S. an estimated 34.5 billion dollars annually. Many invasive species continue to be accidentally introduced to the U.S. as contaminants of crop seeds, spices, produce, packaging and cargo air vents. Once established, such invasive plants often spread undetected through ornamental varieties or mistaken identity of seed and juvenile stages that appear identical to non-invasive varieties. In collaboration with the USDA-APHIS-CPHST, our lab is developing molecular diagnostic techniques that can quickly and cost-effectively identify invasive plant species that are otherwise difficult to identify. Such techniques have had diverse impact, including saving endangered native plant species that were mistakenly identified as their invasive counterparts and the development of automated systems that provide fast and accurate detection of specific species.
Cseke L.J., Wullschleger S., Sreedasyam A., Trivedi G., Larsen P.E., Collart F.R. Chapter 12. Carbon Sequestration. In Genomics and Breeding for Climate-Resilient Crops. Kole C. (ed): Springer, Germany, 2013.
Larsen P.E., Cseke L.J., Collart F.R. (2013) Prediction of an Ectomycorrhizal Metabolome from Transcriptomic Data. In Molecular Microbial Ecology of The Rhizosphere. Frans J. de Bruijn (Ed.); Wiley-Blackwell Publishers.
Larsen P.E., Cseke L.J., Miller M.R., Collart F.R. (2013) Modeling forest ecosystem responses to elevated carbon dioxide and ozone using artificial neural networks. Theoretical Biology (in press).
Cseke, L.J., Talley, S.M. (2012) A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica. JoVE: 3265.
Bazemor, R.A., Feng, J., Cseke, L.J., Podila G.K. (2012) Biomedically important pathogenic fungi detection with volatile biomarkers. Journal of Breath Research 6 (1): 11.
Handbook of Molecular and Cellular Methods in Biology and Medicine-3rd ed., L.J. Cseke, A. Kirakosyan, P.B. Kaufman, M.V. Westfall: CRC Press, Boca Raton, Florida, 2012.
Larsen, P.E., Sreedasyam, A., Trivedi, G., Podila, G.K., Cseke, L.J., Collart, F.R. (2011) Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC Systems Biology 2011, 5:70
Cseke, L.J., Tsai, C-J., Rogers, A., Nelsen, M.P., White, H.L., Karnosky, D.F., Podila, G.K. (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different partitioning patterns under elevated [CO2]: New Phytologist 182: 891–911.
Cseke, L.J., Podila, G.K., Kirakosyan A., Kaufman P. (2009) Plants as Sources of Energy. In Recent Advances in Plant Biotechnology. Kaufman, P.B. and Kirakosyan, A. (eds): Springer, Germany, 2009.
Cseke, L.J., Kaufman, P.B., Kirakosyan A. (2007) The biology of essential oils in the pollination of flowers. Natural Product Communications 2(12): 1317-1336.